b1_afi_notebook.ipynb

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"# I- DESCRIPTION"
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"qMRinfo('b1_afi'); % Describe the model"
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"# II- MODEL PARAMETERS\n",
"## a- Create object"
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"Model = b1_afi;"
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"## Download sample data from OSF\n",
"> The current `Model` is an instance of `b1_afi` class.\n",
" \n",
"You can manually download the sample data for `b1_afi` [by clicking here](https:\/\/osf.io\/csjgx\/download?version=9)."
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"dataDir = downloadData(Model,pwd);"
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"## b- Set protocol\n",
"> Protocol is set according to the example data\n",
" \n",
"%          |- b1_afi object needs 1 protocol field(s) to be assigned:\n",
"%          |-   Sequence"
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"nomFA = 60;\n",
"TR1 = 20;\n",
"TR2 = 100;\n",
"Model.Prot.Sequence.Mat = [ nomFA TR1 TR2];\n",
"%%   "
]
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"# III- FIT EXPERIMENTAL DATASET\n",
"## a- Load experimental data\n",
"%          |- b1_afi object needs 3 data input(s) to be assigned:\n",
"%          |-   AFIData1\n",
"%          |-   AFIData2\n",
"%          |-   Mask"
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"% AFIData1.nii.gz contains [88  128   32] data.\n",
"data.AFIData1=double(load_nii_data('b1_afi_data\/AFIData1.nii.gz'));\n",
"% AFIData2.nii.gz contains [88  128   32] data.\n",
"data.AFIData2=double(load_nii_data('b1_afi_data\/AFIData2.nii.gz'));\n",
" "
]
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"## b- Fit experimental data\n",
"> This section will fit data."
]
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"source": [
"FitResults = FitData(data,Model,0);"
]
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"## c- Show fitting results\n",
"> * Output map will be displayed.\n",
" \n",
"> * If available, a graph will be displayed to show fitting in a voxel."
]
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"cell_type": "code",
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"source": [
"qMRshowOutput(FitResults,data,Model);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## d- Save results\n",
"> * qMR maps are saved in NIFTI and in a structure `FitResults.mat` that can be loaded in qMRLab graphical user interface.\n",
"> * Model object stores all the options and protocol\n",
"> * These objects can be easily shared or be used for simulation."
]
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"cell_type": "code",
"execution_count": null,
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"source": [
"FitResultsSave_nii(FitResults, 'b1_afi_data\/AFIData1.nii.gz');"
]
}
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